A.D. Skinner and Scully are at a standoff when Mulder bursts in and discovers that Skinner has the digital tape. Reunited, Mulder and Scully travel to a secret vault inside a mine and find an elaborate filing system of medical records which reveals that Mulder's sister may not have been the first choice for abduction. Meanwhile, Skinner deals with the Cigarette-Smoking Man for their safety.

The long hidden secret patient of Muir Island, a reality-warping mutant teen known as Proteus, escapes from his 15 year long captivity, and wreaks havoc across Scotland searching out his father.

Liz ends up being held hostage whilst Charlie meets Baz's new husband.

The Warners and Charlton Woodchuck are featured in this parody of of Dr. Seuss's "The Cat In The Hat".

In 1955, Slappy takes Skippy for acting lessons. They go to the Method Actor's Studio. The Studio also features Marlon Brando, James Dean, and Jack Nicholson.